The storage, retrieval, analysis, and interpretation of large amounts of biological data will cross boundaries of all broad biotechnologies. Capability and application range of this tool will continue to increase dramatically. Mining the massively increasing amounts of data at all scales, and integrated analyses and syntheses of these data will greatly increase power to detect genes and understand their functions. The databases developed for sequence and microarray data in particular must be co-ordinated regionally, nationally and internationally, and accessible to the public. Bioinformatics research requires resource-intensive, multidisciplinary teamwork, naturally leading towards more international cooperation over a range of study scales and systems. Opportunities are opening up for developing countries to become involved in these projects.

Proteomic

2

0

Gene Mapping & Markers

3

2

Microarray

2

0

Phenotypic

3

3

Integrated Applications

1

0

Diversity Measurement

mtDNA

2

0

The use of molecular markers for studying natural and artificial forest tree populations has undergone unprecedented expansion due to the vast array of population genetics applications they have enabled. These topics include measurement of genetic diversity within and among populations, comparisons among taxa, historical reconstruction and prediction of species’ range shifts, gene flow, assessment of natural and artificial (e.g., seed orchard) population mating system parameters, introgression and hybridization. Markers have also been used to evaluate the impacts of domestication and silviculture. Genomic and QTL mapping have recently expanded due to the development of unlimited numbers of markers. Anticipated development cost reductions for SNPs will trigger an increase in their use in all forest genetics resources applications.

cpDNA

2

0

RAPD, AFLP, RFLP

3

2

Microsatellite (SSR)

1

0

SNP, ESTP

3

1

Gene Discovery

Phenotypic Traits

3

3

Phenotypic and quantitative trait measurements represent the backbone of all conventional tree breeding. Their proven efficacy and ease of use has resulted in significant gains in many species worldwide.

QTL Mapping

3

1

QTLs will likely increase in importance, particularly for important or hard to measure traits, especially those which require older material for assessments (e.g., all wood properties, disease and insect resistance). The focus is shifting from flanking region markers to markers within the actual gene or QTL of interest.

Genome &

EST Sequencing

2

0

Massive, redundant conifer genomes will restrict sequencing to a few regions of interest. EST sequencing for commercially important species will accelerate within 5 years. Whole genome sequencing has begun for Populus; the data will be freely available; other economically and ecologically important species will follow. International collaboration is important for species whose ranges cross international borders.

Microarray Analysis

2

0

As microarrays become available for gene discovery for growth and yield, wood quality and adaptive attributes (e.g., disease and insect resistance and stress tolerance), more reliable oligo-based will likely replace cheaper clone-based arrays. The potential benefits and challenges will spur international collaboration. This new field is likely to prove most cost-effective for understanding gene function, rapid production technology development for advanced breeding programs and in high yield plantations.

Still in the initial stages, metabolomics asseses the presence/absence of non-protein structural precursors of essential components in biochemical pathways.

Molecular Genetic Modification

Gene Insertion/ Sequence Modification

2

1

Inserting foreign targeted genes into tree genomes has profound potential. This method will enable cross-species gene transfer in cases where it is not possible via conventional breeding. Transformation is widely used in agriculture, but is new to forestry and has engendered major public contention and strict biosecurity protocols for testing and deployment. Some countries and organizations have restricted testing and planting genetically modified trees. Potential for gene escape into wild populations needs further study for risk assessment. Reproduction must be eliminated or postponed past rotation age. This technique could potentially improve fibre yield and quality as well as other important qualitative, quantitative and adaptive attributes.

Gene Targeting/ Knockout

1

0

Silencing gene function is the complement of gene insertion. This technique will expand as the results of microarray and proteomic analyses accrue. Similarly, there is a broad spectrum of potential functional genomics applications and associated ethical issues.

Product Verification

Pedigree Verification

3

3

Development of larger-scale, lower cost application platforms will increase accessibility by genetic improvement programmes to this technology, expanding the prevalent uses: retroactive pedigree verification and verifying clonal identies in seed orchards. Other potential applications include determining the efficacy of seed orchard management techniques on a large scale, and consequent growth and yield determination of resulting crops.

Quality Control/

Quality Assurance

1

0

Rapid developments in product description systems, commonly used in food manufacturing facilities, will result in increasing support for research and application of automated product verification systems. The main technology is PCR-based, e.g., DNA markers to detect mislabelled products (e.g., clones). Functional genomics is expected to yield suites of gene markers that can be used to check process efficiencies during mass production of clonal seedlings.

Cloning

Organogenesis

1

1

Micropropagation (organogenesis) and gametic or somatic embryogenesis require treating tissue explants with growth regulators to induce bud or shoot formation. Most of the shortcomings of organogenesis can be overcome using somatic embryogenesis, but methodology and success are species dependent. These methods are currently in production and cloning will be a significant element in high yield plantation forestry.